JAL-3253 jalview.bin.Instance streamlining

[jalview.git] / src / jalview / io / vamsas / Sequencemapping.java

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 8bea620..bacf8dc 100644 (file)
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -20,12 +20,12 @@
  */
 package jalview.io.vamsas;
 
-import jalview.bin.Instance;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
 import jalview.io.VamsasAppDatastore;
 
 import java.util.ArrayList;
@@ -110,27 +110,32 @@ public class Sequencemapping extends Rangetype
     }
   }
 
+  @Override
   public void addToDocument()
   {
     add(mjvmapping, from, ds);
   }
 
+  @Override
   public void addFromDocument()
   {
     add((SequenceMapping) vobj);
   }
 
+  @Override
   public void conflict()
   {
     conflict(mjvmapping, (SequenceMapping) vobj);
 
   }
 
+  @Override
   public void updateToDoc()
   {
     update(mjvmapping, (SequenceMapping) vobj);
   }
 
+  @Override
   public void updateFromDoc()
   {
     update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj);
@@ -364,9 +369,7 @@ public class Sequencemapping extends Rangetype
       acf.addMap(from, to, mapping);
     }
     bindjvvobj(mapping, sequenceMapping);
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop())
-            .registerMapping(acf);
+    Desktop.getStructureSelectionManager().registerMapping(acf);
     // Try to link up any conjugate database references in the two sequences
     // matchConjugateDBRefs(from, to, mapping);
     // Try to propagate any dbrefs across this mapping.
@@ -402,7 +405,7 @@ public class Sequencemapping extends Rangetype
               + from.getName() + " and " + to.getName());
     }
     List<DBRefEntry> fdb = from.getDBRefs();
-    List<DBRefEntry> tdb = new ArrayList<DBRefEntry>(to.getDBRefs());
+    List<DBRefEntry> tdb = new ArrayList<>(to.getDBRefs());
     int tdblen = to.getDBRefs().size();
 //    
 //